title: compomics-utilities: an open-source Java library for computational proteomics.
abstract: BACKGROUND
  The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool.
  
  
  RESULTS
  In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development.
  
  
  CONCLUSIONS
  As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Norway.
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
authors.forename: Marc
authors.initials: M
authors.lastname: Vaudel
authors.forename: Niklaas
authors.initials: N
authors.lastname: Colaert
authors.forename: Kenny
authors.initials: K
authors.lastname: Helsens
authors.forename: Albert
authors.initials: A
authors.lastname: Sickmann
authors.forename: Frode S
authors.initials: FS
authors.lastname: Berven
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins